The problem is when you attempt to move in another starbase into the a gravwell that has the double base bonus. You can build two (or three or 5 etc) but you cannot move in a starbase if there is already another one there. And its hardcoded. Even an issue with stars.
Yeah, it is this hardcode (which wasn't there originally) that has caused me quite a bit of trouble with Sins of the Sirius Sector.
I had initially envisioned using Starbases as capital ships, allowing them to be upgraded as the player saw fit (and it worked well in my test build), however once that hardcode was applied in an attempt to nerf VR starbases it kind of ruined my plan and I had to change things around.
I wish they would remove the hardcode and just let the starbase limit determine if a starbase can jump.